This should be fixed in today's build. I found the problem last night at the around the same time as someone else (not sure if he is on here). He gets the credit as he raised the patch while I decided to get some sleep. The problem was something that I did for matching the books when a plugboard had been used. It seemed smart at the time, but was pretty stupid now I look at it.
I think there is still some circumstances where the matching will still fail, but they generally mean something else unusual happened as well.